def doReactionAssociation(arguments, output=True): stdOptions = standardOptions() stdOptions.simulation_mode = Literals.trajectory stdOptions.num_simulations = arguments[0] stdOptions.temperature = arguments[1] stdOptions.join_concentration = arguments[2] seq = arguments[3] hybridization(stdOptions, seq, doFirstPassage=True) if len(arguments) > 4: stdOptions.sodium = arguments[4] stdOptions.magnesium = arguments[5] if output: stdOptions.output_interval = 1 stdOptions.simulation_time = A_TIME_OUT stdOptions.simulation_mode = Literals.trajectory i = 65 for state in stdOptions.start_state: for strand in state.strand_list: strand.id = i i += 1 return stdOptions
def create_setup(num_traj, strand_seq): options = standardOptions("First Step", GLOBAL_TEMPERATURE, num_traj, ATIME_OUT) hybridization(options, strand_seq, num_traj) setSaltGao2006(options) return options
def test1(unusedargs): o1 = standardOptions() hybridization(o1, "CCC") o1.simulation_mode = Literals.first_passage_time return o1
def getOptions(trials): o = standardOptions(Options.firstStep, TEMPERATURE, trials, ATIME_OUT) hybridization(o, strand_seq, trials) setSaltGao2006(o) return o
def getOptions(trials): o = standardOptions(Literals.first_step, TEMPERATURE, trials, ATIME_OUT) hybridization(o, strand_seq, trials) setSaltGao2006(o) o.DNA23Metropolis() return o
def getOptions(trials, material): o = standardOptions(Options.firstStep, tempIn=25.0, trials=200, timeOut=0.1) hybridization(o, strand_seq, trials) o.DNA23Metropolis() return o
def getOptions(trials): o = standardOptions(Options.firstPassageTime, TEMPERATURE, trials, ATIME_OUT) hybridization(o, strand_seq, trials, True) setSaltGao2006(o) o.join_concentration = concentration return o
def getOptions(trials): o = standardOptions(Options.firstStep, TEMPERATURE, trials, ATIME_OUT) hybridization(o, strand_seq, trials) setSaltGao2006(o) # setArrheniusConstantsDNA23(o) setArrParams(o, 96) return o
def getOptions(trials): o = standardOptions(Literals.first_passage_time, TEMPERATURE, trials, ATIME_OUT) hybridization(o, strand_seq, trials, True) setSaltGao2006(o) o.join_concentration = concentration o.DNA23Metropolis() return o
def getOptions(trials, material, temperature=25.0, sodium=1.0): o = standardOptions(Literals.first_step, tempIn=temperature, trials=200, timeOut=1.0) o.sodium = sodium hybridization(o, strand_seq, trials) o.DNA23Metropolis() # setArrParams(o, 92) # the best DNA23 parameter set return o
def doSims(strandSeq, numTraj=2): o1 = standardOptions() o1.num_simulations = numTraj o1.output_interval = 1 hybridization(o1, strandSeq) o1.initial_seed = 1777 s = SimSystem(o1) s.start() printTrajectory(o1)
def getOptions( trials, settings ): #start_complex_top, start_complex_bot, success_stop_condition, failed_stop_condition options = standardOptions("First Step", TEMPERATURE, settings.trials, ATIME_OUT) hybridization(options, settings.mySeq, settings.trials) setSaltGao2006(options) options.output_interval = 1 # print every state, ever return options
def getOptions(trials): o = standardOptions(tempIn=float(form_f['temperature']), timeOut=A_TIME_OUT) o.num_simulations = TRIALS hybridization(o, strand_seq, trials) o.sodium = form_f['sodium'] o.magnesium = form_f['magnesium'] o.concentration = 1.0E-9 if "RNA" == form_f['substrate']: o.substrate_type = Literals.substrateRNA return o
def doSims(strandSeq, numTraj=2): o1 = standardOptions() o1.num_simulations = numTraj o1.output_interval = 1 o1.simulation_time = ATIME_OUT # o1.substrate_type = Options.substrateRNA hybridization(o1, strandSeq ) o1.initial_seed = 1777+6 s = SimSystem(o1) s.start() printTrajectory(o1)
def doReaction(arguments): stdOptions = standardOptions() stdOptions.output_interval = 1 stdOptions.simulation_mode = Literals.trajectory stdOptions.join_concentration = 0.001 stdOptions.simulation_time = 400.0 stdOptions.num_simulations = arguments[0] stdOptions.temperature = arguments[2] toggle = arguments[3] if toggle == str_association: hybridization(stdOptions, arguments[1], myTrials=arguments[0], doFirstPassage=True) elif toggle == str_hairpin_closing: hairpinclosing(stdOptions, arguments[1], "TTTTT") elif toggle == str_threeway_strand_displacement: threewayDisplacement(stdOptions, "ACTACG", "AACATGAAGTA", myTrials=arguments[0]) elif toggle == str_dissociation: dissociation(stdOptions, arguments[1], myTrials=arguments[0]) """ Make sure that multistrand IDs equal, everytime. This is required for correctly combining multiple runs. The Multistrand behavior makes sense, but not for this specific use case. """ i = 65 for complex in stdOptions.start_state: for strand in complex.strand_list: strand.id = i i += 1 stdOptions.DNA23Metropolis() return stdOptions